Strain identifier

BacDive ID: 17131

Type strain: Yes

Species: Megasphaera paucivorans

Strain history: <- R. Juvonen <- VTT

NCBI tax ID(s): 1122220 (strain), 349095 (species)

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General

@ref: 6600

BacDive-ID: 17131

DSM-Number: 16981

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative, coccus-shaped

description: Megasphaera paucivorans DSM 16981 is an anaerobe, Gram-negative, coccus-shaped bacterium that was isolated from spoiled Italian beer.

NCBI tax id

NCBI tax idMatching level
349095species
1122220strain

strain history

  • @ref: 6600
  • history: <- R. Juvonen <- VTT

doi: 10.13145/bacdive17131.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Veillonellales
  • family: Veillonellaceae
  • genus: Megasphaera
  • species: Megasphaera paucivorans
  • full scientific name: Megasphaera paucivorans Juvonen and Suihko 2006

@ref: 6600

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Veillonellaceae

genus: Megasphaera

species: Megasphaera paucivorans

full scientific name: Megasphaera paucivorans Juvonen and Suihko 2006

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31505negative1.2-1.9 µm1-1.4 µmcoccus-shapedno
69480negative99.897

colony morphology

  • @ref: 6600
  • incubation period: 3-7 days

pigmentation

  • @ref: 31505
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6600
  • name: MRS pre-reduced (DSMZ Medium 11b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/11b
  • composition: Name: MRS MEDIUM (pre-reduced) (DSMZ Medium 11b) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Resazurin 0.001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
31505positivegrowth15-37
31505positiveoptimum30mesophilic
6600positivegrowth30mesophilic

culture pH

@refabilitytypepH
31505positivegrowth7
31505positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6600anaerobe
31505anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
31505no
69480no99.993

observation

  • @ref: 31505
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3150524265gluconate+carbon source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
3150516136hydrogen sulfideyes
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6600-----------------------------

Isolation, sampling and environmental information

isolation

  • @ref: 6600
  • sample type: spoiled Italian beer
  • country: Italy
  • origin.country: ITA
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Environmental#Microbial community
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_69741.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_37;96_26665;97_37764;98_48985;99_69741&stattab=map
  • Last taxonomy: Megasphaera
  • 16S sequence: DQ223730
  • Sequence Identity:
  • Total samples: 2107
  • soil counts: 125
  • aquatic counts: 1110
  • animal counts: 838
  • plant counts: 34

Safety information

risk assessment

  • @ref: 6600
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Megasphaera paucivorans gene for 16S rRNA, partial sequence, strain: DSM 16981AB6097081184ena349095
6600Megasphaera paucivorans strain VTT E-032341 16S ribosomal RNA gene, partial sequenceDQ2237301553ena349095

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Megasphaera paucivorans DSM 16981GCA_900103535contigncbi349095
66792Megasphaera paucivorans strain DSM 16981349095.5wgspatric349095
66792Megasphaera paucivorans DSM 169812596583540draftimg349095

GC content

  • @ref: 6600
  • GC-content: 40.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno81no
gram-positiveno96.117yes
anaerobicyes99.028yes
halophileno88.492no
spore-formingno88.85yes
glucose-utilyes70.252no
motileno93.552yes
flagellatedno97.144yes
aerobicno97.932yes
thermophileno99.143no
glucose-fermentyes54.034no

External links

@ref: 6600

culture collection no.: DSM 16981, VTT E-032341

straininfo link

  • @ref: 86130
  • straininfo: 290985

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585679Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus.Juvonen R, Suihko MLInt J Syst Evol Microbiol10.1099/ijs.0.63699-02006Beer/*microbiology, Megasphaera/*classification/genetics/isolation & purification/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Pectinatus/*classification, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/analysis/geneticsGenetics
Phylogeny28742009Megasphaera hexanoica sp. nov., a medium-chain carboxylic acid-producing bacterium isolated from a cow rumen.Jeon BS, Kim S, Sang BIInt J Syst Evol Microbiol10.1099/ijsem.0.0018882017Animals, Bacterial Typing Techniques, Base Composition, Carboxylic Acids/*metabolism, Cattle/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Megasphaera/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6600Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16981)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16981
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31505Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127803
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68380Automatically annotated from API rID32A
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
86130Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290985.1StrainInfo: A central database for resolving microbial strain identifiers